“Reverse speciation” (fusion of species) in ravens

Nevermore!

At least a dozen readers have called my attention to a new paper in Nature Communications by Anna M. Kearns et al. (reference at bottom, pdf here), supposedly showing “reverse speciation” in ravens. The paper has received a lot of public attention because it claims to show that two distinct species of ravens have fused back into a single species. And that has excited people because a.) they don’t think this has happened before, and b.) it shows that speciation is not the simple bifurcating tree that Darwin portrayed. Rather, some of the branches can grow back together, fusing into a new single branch.

But, as the authors note, we’ve seen fusion of species before. Often this is connected with anthropogenic habitat change, such as change in climate, local ecology, or the introduction of predators (see a summary paper here). We may be seeing this now with the polar bear and brown bear (“grizzly”). Previously isolated by ecological preference and adaptation (a genetically based “reproductive isolating barrier”), their ecological separation may disappear with climate change. As the brown bear moves north with warmer climate, it will invade the territory of the polar bear, and the two species can hybridize and have done so repeatedly in the wild. If the hybrids are fertile (and I can’t find data on this), the two species may well fuse into one.

But there are other cases of species fusing when humans weren’t responsible. After all, ecological change, climate change, and introduction of predators can occur without the intervention of humans. The problem with finding hybrid species in nature is that one can’t easily detect that they resulted from hybridization if the parental species are both extinct. (The hybrid nature of species is usually detected by seeing that they’re a genetic mosaic of the parental species, and if the parents don’t exist that’s hard to detect.) But we have plenty of example of “hybrid species” that haven’t replaced the parental ones, including many allopolyploid plants as well as diploid hybrid species in butterflies and sunflowers. Further, species do exchange genes more frequently than we used to think, and that “horizontal gene transfer” can mess up phylogenies.

But none of this invalidates the generalization that species nearly always form from geographically isolated populations that genetically differentiate to the point where they can no longer exchange genes, when they’ve evolved barriers to gene exchange like hybrid sterility, ecological preference and adaptation, mate discrimination, and so on. Except in plants, hybrid speciation is the rare exception rather than the rule, and Darwin’s “bifurcating tree” of life, drawn in his notebooks, is still a good description of life:

Now, what did Kearns et al. find? They found that two old lineages of Common Ravens (Corvus corax), one widespread (“Holarctic”) and one from the West coast of North America (“Californian”), had diverged, probably after geographic isolation, about 1.5 million years ago, but then didn’t become two extant species because they began exchanging genes—repeatedly. (The geographic isolation may have resulted from the common ancestor being isolated in refugia during times of glaciation.) So now, in the Western US and Mexico, one finds a raven that looks just like other worldwide ravens, but carries an ancient lineage of genes that must have diverged from the ancestor of “Holarctic” ravens a long time ago. That’s detectable because you find, in that area, birds that carry two gene copies that diverged anciently—far more divergent that the normal variation within Holarctic ravens.

At present, the California and Holarctic forms are not different species because they hybridize readily in Western North America, and there are no two distinct “types”. You can see them in the map below: Holarctic is purple, California is orange, and the hybrids, carrying genes from both, are striped purple-and-orange (the orange type is not found by itself; its genes have simply merged with those of the Holarctic ravens).

The situation is complicated because there’s another species of raven that is “sympatric” (lives in the same area as) both the Holarctic and California ravens but remains distinct: the Chihuahuan Raven, inhabiting the black area below. It’s regarded as a different and full species (Corvus cryptoleucus) because there’s no evidence that it hybridizes with any other group; it appears to be fully reproductively isolated from other ravens.

The distribution of the two lineages (and two species: Common and Chihuahuan) from the paper:

(From paper): (From paper): Reticulate speciation history of North American ravens. a Geographic range of distinct mtDNA lineages within Common and Chihuahuan Ravens based on previous mtDNA studies and range records.

What the authors discovered from DNA sequencing was that in fact the Chihuahuan Raven is more closely related to the California lineage of the Common Raven than to the Holarctic Raven, and apparently split off from the California isolate more recently than the divergence of the Chihuahuan and Holarctic lineages of the single Common Raven. The Chihuahuan branch split off from from the California lineage between 0.6 and 1.5 million years ago.

So what we have is shown in the diagram below: a non-bifurcating family tree. It reflect the ancient divergence of the lineage that produced the Holarctic branch of the Common Raven on one side and the Chihuahuan Raven + California lineage on the other. That branch then split again and more recently, producing the full species the Chihuahuan Raven and then the lineage of Common Raven that fused back with the Holarctic lineage. This should be clear from the diagram:

(From paper): b Hypothesis of speciation reversal where the Common Raven is formed from the fusion of non-sister California (orange) and Holarctic (purple) lineages following secondary contact, while Chihuahuan Ravens (black) remained reproductively isolated despite sympatry with the Common Raven. Dashed lines in b show the mtDNA gene tree topology from this and previous studies. Solid grey background in b traces the changing taxonomic boundaries as the Holarctic lineage first split from the ancestor of the California and Chihuahuan lineages, and then the California and Holarctic lineages fused into a single admixed lineage

The upshot: The big question, and the reason this paper got so much publicity, is the claim, echoed in the paper’s title, that it showed “speciation reversal.” That is, the authors assume that the California lineage was once a species of raven distinct from the Holarctic Common Raven, but then fused with it later. Somehow the reproductive barriers (genetic ones) that kept them apart became ineffectual.

That, of course, assumes that there were once reproductive barriers between the California and Holarctic lineages. But we have no evidence for that! The fact that they fused so easily, and without human intervention, argues against substantial reproductive barriers, though there could have been some ecological ones. The authors simply assume that, because the Chihuahuan raven became a full species in less time than the Holarctic-California divergence, then the latter divergence must ALSO have involved full speciation.

But divergence time tells us very little about speciation. The key is whether a lineage evolves reproductive barriers from another one, not how long they’ve been separated. And those reproductive barriers are probably byproducts of selection, which can be either strong or weak. That’s why, when judging whether two populations are biological species, evolutionists prefer to use indices of reproductive isolation (observations of no matings, no evidence of genetic admixture) rather than divergence times. It may be, with the Holarctic and California lineages, that they simply didn’t diverge genetically enough to produce reproductive barriers as a byproduct. That’s what happened to Homo sapiens: our own geographic isolates in Polynesia, Australia, and the New World weren’t separated long enough from the rest of the species to become new species of humans. Now that we have transportation and migration, we’re in the process of slowly fusing into one big gene pool, which may never be fully mixed but mixed enough to keep us able to mate with people from every other place.

The authors recognize this problem but, perhaps recognizing the extra attention that “speciation reversal” will get (as opposed to “lineage reversal”), make the flawed “time argument” for speciation (my emphasis in the quote):

Thus, it is not clear-cut whether we should call the situation in ravens ‘speciation reversal’ or view it as a case of ‘ancient lineage fusion’. This contrasts with most other examples of speciation reversal, where there is strong evidence for the strength and nature of reproductive isolation prior to speciation reversal despite a very shallow divergence between lineages (e.g., sticklebacks). Two lines of evidence suggest that California and Holarctic lineages could have been reproductively isolated prior to secondary contact and lineage fusion. First, the timing of divergence of the Holarctic lineage and the ancestor of the California and Chihuahuan lineages between 0.9 and 2 mya (Supplementary Fig. 1) is approaching the limit where most bird taxa (especially those in the northern hemisphere) have evolved reproductive isolation (~2 mya). Second, life history traits, as well as mtDNA, intron, SNP and ENM analyses all support reproductive isolation between Chihuahuan Ravens and Common Ravens despite the more recent divergence of the Chihuahuan Raven and the California lineage 0.6–1.5 mya (Supplementary Fig. 1). This shows that ravens can develop reproductive isolation and maintain strong species boundaries after a more recent divergence than that between California and Holarctic lineages. We argue that our findings represent the strongest support possible for the conclusion of speciation reversal given the inability to measure ancient prefusion reproductive isolation.

I am not convinced by either line of evidence that the Holarctic and California lineages were separate species. Speciation times can vary among taxa, and if selection is weak, lineages may not progress to full species for a very long time. Using data from other birds doesn’t settle the issue in this particular case. The second line of evidence isn’t really independent: the authors simply say that because the Chihuahuan Raven speciated in less time than the divergence between Holarctic and California lineages, the latter two must also have been species. That’s not convincing either. “Time to speciation” varies widely, even within a group, depending on various factors that include the strength of selection, the degree of geographic isolation, and so on.

So what we see here is lineage fusion, not species fusion. Even the authors recognize the problem in the bolded bit above, but they try to obviate that. Pity that the science journalists who wrote about this didn’t know much about speciation.

maybe there is a lesson here, that we should differentiate in our writing and teaching more carefully between:
1. differentiated populations that can hybridize (and sometimes don’t hybridize for reasons other than evolved reproductive isolation mechanisms);
2. separate species that evolved reproductive isolation mechanisms;
3. gray-zone cases where we don’t know whether there was, or was not, evolution of reproductive isolation mechanisms (and therefore we should not obsess too religiously about sorting out such cases, or hype them up with terminology like “speciation reversal”).

Each of the above three are actually “lineages”, and differentiating between “lineage fusion” versus “species fusion” may not clarify the key issues here.

I have the same question and am curious about how the parent species “finally” becomes reproductively isolated from the fertile hybrid. I read the first polar bear post Michael provided and it didn’t help clarify for me. Also, is a group paraphyletic because the excluded groups were classified in error or because of something else?

It’s very complex; I recommend you read a good textbook on Evolution (e.g. Futuyma’s) to see how this happens, or, if you’re a biologist, my own book, which is for grad students and professionals.

A paraphyletic group is paraphyletic because the true phylogeny wasn’t known when it was created; it contains groups or species that are more closely related to OTHER groups than to groups (or species) within the “paraphyletic” group.

A paraphyletic group includes another group given another name at the same rank.

Think of a group that branches into groups A, B, and C. A and C look alike, and you all them species 1. B looks different, and you give it a new name. However, it turns out that the branching first produced group A and (B+C). Only later did the second group branch into separate group B and group C. (Draw this with lines showing the split.)

Naming a paraphyletic group is now considered bad practice. However, I defend paraphyletic groups sometimes. (See my next two comments.)

Where do species come from? Other species. Do they some from the whole ancestral species, or only part of it? Usually only part.

Species 1 consists of populations A, B, C, D, E, F, G, H, I, J, etc. Interbreeding occurs often enough between the populations that they are all clearly one species.

Part of population F gets cut off for a while, forming population 2. Conditions are different, mutations are different, small population size makes chance changes important. After a bit, population 2 becomes unable to breed with the rest of F, or any of the other lettered populations. Population 2 is now species 2.

Meanwhile, species 1 with all of its populations goes along, undisturbed. Species 1 is now paraphyletic to population 2. And that’s OK. This pattern is common in speciation, and even die-hard cladists (i.e., rabid anti-paraphylists) accept that, though it pains them to do it.

Example? A pair of Lomatium (biscuitroot or desert parsley) species that colleagues are going to write up as two species.

Thank you. This makes sense. The “part of population F – 2 is now species 2” is extremely helpful. That is very clear. I drew the A, B, and C diagram with two lines coming from one circle (blank circle) to circle A and circle B+C. There are two lines coming from circle B + C, one to circle B and one to circle C. B is supposed to look different so I guess I’m wondering if the “excluded” groups that “look like” B would be other letters or within the letters already on the diagram. I should be able to figure it out with a textbook and/or after reading your second comment. Thank you so much.

Sometimes the “species 2” of the comment above becomes very different morphologically. Sometimes it produces descendants so different we’d like to call them a different genus. Here we get into a more subjective situation.

I personally think that although our taxonomic (naming) system should reflect phylogeny (evolutionary relationships), taxonomy isn’t phylogeny. Sometimes we have to remember taxonomy is supposed to be a practical guide to classifying and remember organisms.

However, I do not rule the world (unfortunately for the world), so the shooting stars are being renamed as species of Primula. Sigh.

I would have no idea whether or not to group them in the same genus based on a visual observation. I would guess maybe the same order. If I understand correctly, dodecatheon hendersinii would be like the letter F in the other comment and the certain species of Primula would be like the remaining group of F that isn’t able to reproduce anymore with dodecatheon hendersonii. Should dodecatheon hendersonii be in the genus Primula? I really didn’t know until I read the rest of the comment. I don’t know. I would agree that the classification would make sense to include the phylogeny. It seems like it would make sense for that specific species of the genus Primula to be the genus for dodecatheon hendersonii and the species that branch off of that (I just read there are species from that species). Very interesting. Now I’m curious about the relationship between taxonomy and phylogeny. One thing at a time. Thank you again.

Are any eucaryote groups strictly monophyletic? I know I’m not, and I doubt that anyone else is either. Personally, I’m polyphyletic, but I still have a name and I’m still a (small) natural group, even if the mitochondria members of my group aren’t all that closely related to the rest of me.

I think we need to be relaxed about this monophyletic-polyphyletic-paraphyletic stuff. Perhaps we should just make clear why we’re grouping things the way we are, and let it go at that.

When I first started reading the post I kept having an intrusive thought about Dollo’s law, but a quick glance at the wikipedia may have set me straight. The so-called law of irreversability seems more about character states than alleged or incipient speciation events. We are committed to pharyngeal clefts and notochords and probably won’t be reverting away from that anytime soon. And going back to the state represented by lancelets is out of the question. But fusing with Neanderthals is open to possibility. Not sure about manpanzees.

Still can’t shake the notion that drift is important to speciation. Maybe clinging to the genetic revolution in peripheral isolates notion which I might cast blame for on Papa Ernst (pbuh). You seem to take a selectionist view on speciation. I know you wrote a book on it, but old notions are hard to shake.

I agree that drift can be important in speciation. Selection can be very important if species A and B get back together and hybridize, and the hybrids are poorly adapted. Then there will be strong selection against interbreeding. Often, though, that doesn’t happen to any great extent. Often, inability to interbreed is a side effect of changes that happen for other reasons, sometimes selection, often just chance changes.

They were apparently just using some other species definition than biological — probably one of the lineage concepts, wherein every cladelet could become a species. There are at east a dozen species concepts in use, and some people are deeply hostile to the BSC for some reason.

It appears to me that a great deal depends on what one would call a species. If they can ‘fuse’ back again, they are/were not really proper different species. That is, of course, somewhat begging the question.

Well, that depends. Polars and grizzlies were good species AT ONE TIME because they had genetically based ecological isolating barriers based on habitat preference. But their habitats are converging, and so two “good” species can fuse back into one. If that happens, of course.

Thanks, very interesting! This takes me back to the problem with the neanderthals: a subspecies or a different species? We didn’t fuse easily with them (the genetical admixture is so small). And they went extinct. And there seems to be an ecological niche difference. Would’t this make it more sensible to treat them as a different species.

This is a great post. I am surprised this phenomena does not occur more often. I also think that the outcome is almost certainly not the original, though it could be. Classically cloning is aloud.

If A forms into B and C (speciation) and then B and C form into D (reverse speciation), D could be A, but D could be different from A.

Likewise, If I were to reproduce with a female from 2000 years ago (same species) I know my offspring would have some anomalous traits not seen in most people today: possibly shorter, poor verbal comprehension, but greater strength and greater spatial memory, etc..

…2000 years ago (same species) I know my offspring would have some anomalous traits not seen in most people today: possibly shorter, poor verbal comprehension, but greater strength and greater spatial memory, etc…

I strongly doubt this – you’re missing one zero or two or three.

I would bet a lot of money that people from 18AD [140 generations ago say] were intellectually skilled in ways that have fallen out of fashion due to our ‘literacy’ & multiple recording technologies. Examples: Recitation of passed down legends, myths, poetry, drinking songs etc.

I doubt there would be any noticeable difference on average in any of the qualities you mention over two thousands of years – if kiddo is raised on a modern diet & socialised like us [for all values of “us” including Norfolk]

The Holarctic and Californian ravens sort of remind me of Homo sapiens sapiens and H. sapeins neanderthalis. Formerly separated populations of humans, not yet really speciated, merged together again where they co-existed.

Well, they didn’t really merge in the sense of creating a hybrid “swarm”: a few Neanderthals mated with “modern humans”, and those “hybrids” backcrossed again to modern humans, but most Neanderthals simply went extinct without leaving offspring, not “pseudoextinction” via mass mating.

Mary Barkworth, grass taxonomist at Utah State University, calls this “despeciation.” It occurs in plants. It’s especially common when old-world species that are geographically isolated in the old world and behave very nicely as species, are introduced to the New World, meet, and hybridize, producing fertile offspring. Tamarisk does it, and certain grasses.

Speciation seems a bit of a trick. There are various potential isolating mechanisms. The biological species concept is popular. Whether hybrids are fertile is an important consideration with Jerry’s uncertainty about polarXbrown bears.

It seems a matter of probability of circumstances where two members of putatively different species will mate and given that will tend to produce fertile offspring. Is the latter consideration black/white or gray? If I recall in sea turtles members of different genera can mate and produce offspring, but no idea on hybrid fertility.

Turtles are weird creatures anyway due to uncertainty of ohylogenetic placement and to a somewhat heavily discrete morphological shift in development resulting in changed placement of scapula and ribs versus other verts. Olivier Rieppel has an excellent book on oddball turtles called “Turtles as hopeful monsters”. Another developmentally anomolous group are the geomyid rodents that develop external pouches.

Getting back to speciation itself isn’t that a matter of people imposing discrete categories upon situations that are usually imperceptibly blended such as defining sand heaps and baldness (Sorites)?

In most cases, the process of speciation begins with populations being obviously the same species and ends with them being obviously different species, but in between is a gray area where they’re sort of different but not yet completely isolated.

Less common methods of speciation (e.g. chromosome doubling, or chromosome rearrangement) can lead to reproductive isolation in a single generation.

Your diagram looks to me like a Feynman diagram, which (if you didn’t already know) is (roughly speaking) a pictorial representation of an interaction between subatomic particles.

The idea is that when an interaction occurs, a variety of things might be happening under the quantum-mechanical covers. Since it’s quantum mechanics we’re talking about we can’t be sure that any of those interactions do actually happen, but we know the end result any way. We just have probabilities for each of the possible interactions.

The analogy I’m making here is that end result, speciation-wise, is “known” to be two species, Common and Chihuahuan Raven. There’s a few ways that the speciation could have occurred, and your diagram is one of them. One of the less probable ones, actually (I think), which would be it’s an interesting result.

However in speciation we can actually look at the result and determine what happened. That’s not the case in quantum mechanics. But no analogy is perfect, right?

I am probably wrong, but fusion looks like just a form of hybridization to me. If two species have gametic isolation, they can neither hybridize or fuse. Gametic isolation is common, which is why Darwin’s diagram is prevalent.